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When Yoshi starts the level, he will be in an outdoor fortress area with a huge moon, hills and skinny trees in the background. He will then need to cross a long gap as the Helicopter. Along the way, Yoshi must avoid the Skeleton Goonies; crashing into them will cause him to fall (usually leading to losing a life). Kamek will also fly in, trying to knock Yoshi out of the sky. If Yoshi makes it to the Yoshi Block (followed by a Middle Ring), Kamek will fly in for the last time in the area and look at Yoshi grimly.

The hallway inside the castle consists of four areas to choose from (doors on a roulette wheel). Four doors which are numbered 1, 2, 3 and 4 spin on the wheel, and Yoshi must pelt one with a Yoshi Egg, which will then drop to the floor and allow him to progress.

Door 3 is notable for the appearance of Tap-Tap the Golden. He will chase Yoshi through a lava-filled cave path that autoscrolls. Yoshi can knock Tap-Tap the Golden back and into a pit with eggs, buying him some time. Tap-Tap the Golden will eventually reappear on screen, however. Eventually, Yoshi will reach a Warp Pipe to get away from him.

Door 4 consists mostly of moving platforms that hold Coins (being a coin path where the player can get a lot of extra lives). The only possible threats are a few Gusties that fly through the stage and two Fly Guys at the end who carry 1-Ups.

All four areas lead to the final room. The final room before the boss battle is an autoscrolling playroom. Kamek will appear, desperately trying to blast Yoshi with his magic wand. If Kamek hits any of the blocks in the level, they will turn into a Fang, a Milde, a Shy Guy, or a Star. If Yoshi makes it past Kamek's final shots, he will be awarded with a Middle Ring and a huge door that leads to Baby Bowser's room.

Kamek will greet Yoshi, demanding he hand over Baby Mario. Soon, however, Baby Bowser will awake, aggravated that Kamek "woke" him. He will repeatedly Ground Pound Kamek and then kick him aside, before noticing Yoshi and acknowledging him as a "gween donkey". He will attack Yoshi, trying to push Baby Mario off and ride Yoshi. Yoshi must dodge Baby Bowser's Ground Pounds and Ground Pound the floor himself, creating a shockwave that can damage the young Koopa King.

Once Baby Bowser is defeated, Kamek will return, fully healed from his beating, and put his magic to its full power. Yoshi then finds himself in the now-destroyed room, and a giant Baby Bowser will appear in the background. Yoshi must nab red Giant Yoshi Eggs from the Balloons that fly in, while avoiding falling rocks that destroy the stadium, fireball blasts from the gigantic Baby Bowser, and Baby Bowser charging at Yoshi head on. If Yoshi hits him enough times, Baby Bowser is returned to his normal self, and Kamek will fly off with him. Then, Yoshi jumps up to a small area where the stork and Baby Luigi are kidnapped. After that, a message says:

Thus, due to the marvelous team work of the Yoshi clan, the twins are reunited.

The captured stork is freed by Yoshi, and sets about his duty and finally makes the long awaited delivery!

Thank you, Yoshi! The twins will meet the parents soon!

The Stork can then make his delivery to Baby Mario and Luigi's mother and father, and the credits roll.